Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

Wenyan Nong, Jianquan Cao, Yiqian Li, Zhe Qu, Jin Sun, Thomas Swale, Ho Yin Yip, Pei Yuan Qian, Jian-Wen Qiu, Hoi Shan Kwan, William Bendena, Stephen Tobe, Ting Fung Chan, Kevin Y. Yip, Ka Hou Chu, Sai Ming Ngai, Karl Yk Tsim, Peter W. H. Holland () and Jerome H. L. Hui ()
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Wenyan Nong: The Chinese University of Hong Kong
Jianquan Cao: The Chinese University of Hong Kong
Yiqian Li: The Chinese University of Hong Kong
Zhe Qu: The Chinese University of Hong Kong
Jin Sun: The Hong Kong University of Science and Technology
Thomas Swale: Dovetail Genomics
Ho Yin Yip: The Chinese University of Hong Kong
Pei Yuan Qian: The Hong Kong University of Science and Technology
Jian-Wen Qiu: Hong Kong Baptist University
Hoi Shan Kwan: The Chinese University of Hong Kong
William Bendena: Queen’s University
Stephen Tobe: University of Toronto
Ting Fung Chan: The Chinese University of Hong Kong
Kevin Y. Yip: The Chinese University of Hong Kong
Ka Hou Chu: The Chinese University of Hong Kong
Sai Ming Ngai: The Chinese University of Hong Kong
Karl Yk Tsim: Hong Kong University of Science and Technology
Peter W. H. Holland: University of Oxford
Jerome H. L. Hui: The Chinese University of Hong Kong

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.

Date: 2020
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DOI: 10.1038/s41467-020-16801-9

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